Beadchip technology to detect DNA methylation in mouse faithfully recapitulates whole-genome bisulfite sequencing

Aim: To facilitate wide-scale implementation of Illumina Mouse Methylation BeadChip (MMB) technology, array-based measurement of cytosine methylation was compared with the gold-standard assessment of DNA methylation by whole-genome bisulfite sequencing (WGBS). Methods: DNA methylation across two mouse strains (C57B6 and C3H) and both sexes was assessed using the MMB and compared with previously existing deep-coverage WGBS of mice of the same strain and sex. Results & conclusion: The findings demonstrated that 93.3-99.2% of sites had similar measurements of methylation across technologies and that differentially methylated cytosines and regions identified by each technology overlap and enrich for similar biological functions, suggesting that the MMB faithfully recapitulates the findings of WGBS.

Automated summary

This study compared the DNA methylation assessment using Illumina Mouse Methylation BeadChip (MMB) technology with the gold-standard method of whole-genome bisulfite sequencing (WGBS). The results showed that MMB produced similar measurements of methylation as WGBS, and the differentially methylated cytosines and regions identified by both methods overlapped and enriched for similar biological functions, indicating that MMB faithfully recapitulates the findings of WGBS.